data_3FC9
#
_model_server_result.job_id            AeSnie4ZQ16paKhPkkaG1A 
_model_server_result.datetime_utc      '2024-11-24 08:41:13' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3fc9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":143}' 
#
_entry.id    3FC9 
#
_exptl.entry_id    3FC9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            3FC9 
_cell.length_a            82.586 
_cell.length_b            153.043 
_cell.length_c            184.786 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3FC9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,H,I,P,Q,R,S,W 1 1,2 
C,D,E,J,K,L,M,N,O,T,U,V 2 1,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_656 -x+1,y,-z+3/2 -1 0 0 0 1 0 0 0 -1 82.586 0 277.179 
3 'crystal symmetry operation' 4_567 x,-y+1,-z+2 1 0 0 0 -1 0 0 0 -1 0 153.043 369.572 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 I N N 
? 4 K N N 
? 4 M N N 
? 4 O N N 
? 4 Q N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 H MG MG . B MG 142 1_555 I O1A CDP . B CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc2 H MG MG . B MG 142 1_555 I O2B CDP . B CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc3 J MG MG . C MG 142 1_555 K O1A CDP . C CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc4 J MG MG . C MG 142 1_555 K O2B CDP . C CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc5 L MG MG . D MG 142 1_555 M O2B CDP . D CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc6 L MG MG . D MG 142 1_555 M O1A CDP . D CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc7 N MG MG . E MG 142 1_555 O O1A CDP . E CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc8 P MG MG . F MG 142 1_555 Q O2B CDP . F CDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
#
_chem_comp.formula           'C9 H15 N3 O11 P2' 
_chem_comp.formula_weight    403.176 
_chem_comp.id                CDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
O3B PB CDP sing 70 n n 
PB O1B CDP doub 71 n n 
PB O2B CDP sing 72 n n 
PB O3A CDP sing 73 n n 
O3A PA CDP sing 74 n n 
PA O1A CDP doub 75 n n 
PA O2A CDP sing 76 n n 
PA O5' CDP sing 77 n n 
O5' C5' CDP sing 78 n n 
C5' C4' CDP sing 79 n n 
C5' "H5'1" CDP sing 80 n n 
C5' "H5'2" CDP sing 81 n n 
C4' O4' CDP sing 82 n n 
C4' C3' CDP sing 83 n n 
C4' H4' CDP sing 84 n n 
O4' C1' CDP sing 85 n n 
C3' O3' CDP sing 86 n n 
C3' C2' CDP sing 87 n n 
C3' H3' CDP sing 88 n n 
O3' HA CDP sing 89 n n 
C2' O2' CDP sing 90 n n 
C2' C1' CDP sing 91 n n 
C2' H2' CDP sing 92 n n 
O2' HB CDP sing 93 n n 
C1' N1 CDP sing 94 n n 
C1' H1' CDP sing 95 n n 
N1 C2 CDP sing 96 n n 
N1 C6 CDP sing 97 n n 
C2 O2 CDP doub 98 n n 
C2 N3 CDP sing 99 n n 
N3 C4 CDP doub 100 n n 
C4 N4 CDP sing 101 n n 
C4 C5 CDP sing 102 n n 
N4 H4N1 CDP sing 103 n n 
N4 H4N2 CDP sing 104 n n 
C5 C6 CDP doub 105 n n 
C5 H5 CDP sing 106 n n 
C6 H6 CDP sing 107 n n 
HO1 O2A CDP sing 108 n n 
HO2 O2B CDP sing 109 n n 
HO3 O3B CDP sing 110 n n 
#
_atom_sites.entry_id                     3FC9 
_atom_sites.fract_transf_matrix[1][1]    0.012109 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006534 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.005412 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
G 2 CTP A 1 142 1 CTP CTP . 
H 3 MG B 1 142 1 MG MG . 
I 4 CDP B 1 143 1 CDP CDP . 
J 3 MG C 1 142 1 MG MG . 
K 4 CDP C 1 143 1 CDP CDP . 
L 3 MG D 1 142 1 MG MG . 
M 4 CDP D 1 143 1 CDP CDP . 
N 3 MG E 1 142 1 MG MG . 
O 4 CDP E 1 143 1 CDP CDP . 
P 3 MG F 1 142 1 MG MG . 
Q 4 CDP F 1 143 1 CDP CDP . 
R 5 HOH A 1 143 17 HOH HOH . 
R 5 HOH A 2 144 19 HOH HOH . 
R 5 HOH A 3 145 55 HOH HOH . 
S 5 HOH B 1 144 3 HOH HOH . 
S 5 HOH B 2 145 4 HOH HOH . 
S 5 HOH B 3 146 24 HOH HOH . 
S 5 HOH B 4 147 26 HOH HOH . 
S 5 HOH B 5 148 28 HOH HOH . 
S 5 HOH B 6 149 32 HOH HOH . 
S 5 HOH B 7 150 33 HOH HOH . 
S 5 HOH B 8 151 34 HOH HOH . 
S 5 HOH B 9 152 36 HOH HOH . 
S 5 HOH B 10 153 38 HOH HOH . 
S 5 HOH B 11 154 42 HOH HOH . 
S 5 HOH B 12 155 48 HOH HOH . 
S 5 HOH B 13 156 50 HOH HOH . 
S 5 HOH B 14 157 54 HOH HOH . 
T 5 HOH C 1 144 8 HOH HOH . 
T 5 HOH C 2 145 11 HOH HOH . 
T 5 HOH C 3 146 12 HOH HOH . 
T 5 HOH C 4 147 15 HOH HOH . 
T 5 HOH C 5 148 25 HOH HOH . 
T 5 HOH C 6 149 35 HOH HOH . 
T 5 HOH C 7 150 39 HOH HOH . 
T 5 HOH C 8 151 41 HOH HOH . 
T 5 HOH C 9 152 45 HOH HOH . 
T 5 HOH C 10 153 52 HOH HOH . 
U 5 HOH D 1 144 1 HOH HOH . 
U 5 HOH D 2 145 2 HOH HOH . 
U 5 HOH D 3 146 10 HOH HOH . 
U 5 HOH D 4 147 13 HOH HOH . 
U 5 HOH D 5 148 16 HOH HOH . 
U 5 HOH D 6 149 18 HOH HOH . 
U 5 HOH D 7 150 21 HOH HOH . 
U 5 HOH D 8 151 30 HOH HOH . 
U 5 HOH D 9 152 46 HOH HOH . 
U 5 HOH D 10 153 49 HOH HOH . 
U 5 HOH D 11 154 51 HOH HOH . 
U 5 HOH D 12 155 57 HOH HOH . 
V 5 HOH E 1 144 6 HOH HOH . 
V 5 HOH E 2 145 14 HOH HOH . 
V 5 HOH E 3 146 23 HOH HOH . 
V 5 HOH E 4 147 27 HOH HOH . 
V 5 HOH E 5 148 29 HOH HOH . 
V 5 HOH E 6 149 31 HOH HOH . 
V 5 HOH E 7 150 44 HOH HOH . 
V 5 HOH E 8 151 56 HOH HOH . 
W 5 HOH F 1 144 5 HOH HOH . 
W 5 HOH F 2 145 7 HOH HOH . 
W 5 HOH F 3 146 9 HOH HOH . 
W 5 HOH F 4 147 20 HOH HOH . 
W 5 HOH F 5 148 22 HOH HOH . 
W 5 HOH F 6 149 37 HOH HOH . 
W 5 HOH F 7 150 40 HOH HOH . 
W 5 HOH F 8 151 43 HOH HOH . 
W 5 HOH F 9 152 47 HOH HOH . 
W 5 HOH F 10 153 53 HOH HOH . 
W 5 HOH F 11 154 58 HOH HOH . 
W 5 HOH F 12 155 59 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O3B CDP . . . O 4 32.838 61.289 168.418 1 26.7 ? O3B CDP 143 E 1 
HETATM 2 P PB CDP . . . O 4 31.816 61.869 167.467 1 25.23 ? PB CDP 143 E 1 
HETATM 3 O O1B CDP . . . O 4 31.467 63.31 167.789 1 27.11 ? O1B CDP 143 E 1 
HETATM 4 O O2B CDP . . . O 4 32.044 61.646 165.983 1 29.47 ? O2B CDP 143 E 1 
HETATM 5 O O3A CDP . . . O 4 30.503 60.977 167.825 1 32.5 ? O3A CDP 143 E 1 
HETATM 6 P PA CDP . . . O 4 29.549 60.145 166.801 1 27.14 ? PA CDP 143 E 1 
HETATM 7 O O1A CDP . . . O 4 29.975 60.325 165.356 1 27.53 ? O1A CDP 143 E 1 
HETATM 8 O O2A CDP . . . O 4 29.355 58.763 167.383 1 24.58 ? O2A CDP 143 E 1 
HETATM 9 O O5' CDP . . . O 4 28.146 60.873 167.06 1 28.4 ? O5' CDP 143 E 1 
HETATM 10 C C5' CDP . . . O 4 27.817 62.137 166.506 1 30.84 ? C5' CDP 143 E 1 
HETATM 11 C C4' CDP . . . O 4 27.255 62.932 167.675 1 31.92 ? C4' CDP 143 E 1 
HETATM 12 O O4' CDP . . . O 4 25.962 62.444 168.044 1 34.82 ? O4' CDP 143 E 1 
HETATM 13 C C3' CDP . . . O 4 28.111 62.797 168.922 1 29.22 ? C3' CDP 143 E 1 
HETATM 14 O O3' CDP . . . O 4 29.091 63.83 168.941 1 30.11 ? O3' CDP 143 E 1 
HETATM 15 C C2' CDP . . . O 4 27.123 62.95 170.058 1 31.62 ? C2' CDP 143 E 1 
HETATM 16 O O2' CDP . . . O 4 27.086 64.312 170.482 1 32.17 ? O2' CDP 143 E 1 
HETATM 17 C C1' CDP . . . O 4 25.77 62.61 169.451 1 32.23 ? C1' CDP 143 E 1 
HETATM 18 N N1 CDP . . . O 4 25.279 61.345 170.001 1 32.47 ? N1 CDP 143 E 1 
HETATM 19 C C2 CDP . . . O 4 24.102 61.333 170.778 1 36.42 ? C2 CDP 143 E 1 
HETATM 20 O O2 CDP . . . O 4 23.487 62.408 170.966 1 38.61 ? O2 CDP 143 E 1 
HETATM 21 N N3 CDP . . . O 4 23.637 60.172 171.309 1 35.36 ? N3 CDP 143 E 1 
HETATM 22 C C4 CDP . . . O 4 24.314 59.018 171.094 1 34.59 ? C4 CDP 143 E 1 
HETATM 23 N N4 CDP . . . O 4 23.855 57.858 171.619 1 33.19 ? N4 CDP 143 E 1 
HETATM 24 C C5 CDP . . . O 4 25.483 59.016 170.333 1 32.49 ? C5 CDP 143 E 1 
HETATM 25 C C6 CDP . . . O 4 25.958 60.209 169.799 1 31.03 ? C6 CDP 143 E 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#